title: Cactus graphs for genome comparisons.
abstract: We introduce a data structure, analysis, and visualization scheme called a cactus graph for comparing sets of related genomes. In common with multi-break point graphs and A-Bruijn graphs, cactus graphs can represent duplications and general genomic rearrangements, but additionally, they naturally decompose the common substructures in a set of related genomes into a hierarchy of chains that can be visualized as two-dimensional multiple alignments and nets that can be visualized in circular genome plots. Supplementary Material is available at www.liebertonline.com/cmb .
authors.affiliation: Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California, USA. benedict@soe.ucsc.edu
authors.forename: Benedict
authors.initials: B
authors.lastname: Paten
authors.forename: Mark
authors.initials: M
authors.lastname: Diekhans
authors.forename: Dent
authors.initials: D
authors.lastname: Earl
authors.forename: John St
authors.initials: JS
authors.lastname: John
authors.forename: Jian
authors.initials: J
authors.lastname: Ma
authors.forename: Bernard
authors.initials: B
authors.lastname: Suh
authors.forename: David
authors.initials: D
authors.lastname: Haussler
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D003196:Computer Graphics; D004247:DNA / Q000235:genetics; D019143:Evolution, Molecular; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*
chemical_list: D004247:DNA